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Sample GSM6697094 Query DataSets for GSM6697094
Status Public on May 01, 2023
Title K562 circMLLT1e2 1
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
cell type: CML
genotype: cell line
treatment: Transgenic line
passage: 6-10
Treatment protocol Cells stably transduced with lentivirus were selected on the basis of GFP expression encoded on the pMIG plasmid by flow cytometry. Cell populations with GFP expression >99% were used for experiments.
Cells were xenografted into NSG mice (6-8 per group) in a single-blinded experiment. Mouse welfare was tracked and weekly bleeds were performed to look at prpoportion of human GFP cells in the circulation. Mice were euthanised as a result of tumour cell burden and cells were collected, and following RBC lysis, were sorted by flow cytometry for GFP expression. Cell lines were made and frozen down within 72hrs post-collection.
Growth protocol K562 and HL-60 cells stably expressing transgenic constructs were cultivated in RPMI1640 medium with 10% FBS at 37oC with 5% carbon dioxide
Extracted molecule total RNA
Extraction protocol RNA was extracted with TRIzol and purified with Zymo RNA purfiication kit with on-column DNaseI digestion.
NEBNext UltraII Directional RNA sequencing kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description SC8
SC1_SC46_RawCounts.xlsx
Data processing Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 (Martin, 2011), setting minimum-length option to 18, error-rate 0.2 and overlap 5.
The resulting FASTQ files for total RNAseq respectively were analysed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (Dobin et al., 2013) (version 2.5.3a with default parameters and --chimSegmentMin 20).
The resulting STAR produced Chimeric.out.junction file for each sample was parsed and annotated for circRNA prediction and backsplice abundance using CIRCexplorer2 (Zhang et al., 2016).
Alignments were visualised and interrogated using the Integrative Genomics Viewer v2.3.80 (Thorvaldsdóttir et al., 2013).
Assembly: hg19
 
Submission date Oct 30, 2022
Last update date May 01, 2023
Contact name Simon Conn
E-mail(s) simon.conn@flinders.edu.au
Organization name Flinders University
Department College of Medicine and Public Health
Lab Circular RNAs in Cancer Laboratory
Street address Sturt Road, Bedford Park
City Adelaide
State/province South Australia
ZIP/Postal code 5042
Country Australia
 
Platform ID GPL16791
Series (2)
GSE125986 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability
GSE216873 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [RNA-seq 2]
Relations
BioSample SAMN31526831
SRA SRX18082375

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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